DOCSLIB.ORG

Oscaf2 Contains Two CRM Domains and Is Necessary for Chloroplast

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Oscaf2 Contains Two CRM Domains and Is Necessary for Chloroplast Shen et al. BMC Plant Biology (2020) 20:381 https://doi.org/10.1186/s12870-020-02593-z RESEARCH ARTICLE Open Access OsCAF2 contains two CRM domains and is necessary for chloroplast development in rice Lan Shen1†, Qiang Zhang1†, Zhongwei Wang2, Hongling Wen1, Guanglian Hu1, Deyong Ren1, Jiang Hu1, Li Zhu1, Zhenyu Gao1, Guangheng Zhang1, Longbiao Guo1, Dali Zeng1 and Qian Qian1* Abstract Background: Chloroplasts play an important role in plant growth and development. The chloroplast genome contains approximately twenty group II introns that are spliced due to proteins encoded by nuclear genes. CAF2 is one of these splicing factors that has been shown to splice group IIB introns in maize and Arabidopsis thaliana. However, the research of the OsCAF2 gene in rice is very little, and the effects of OsCAF2 genes on chloroplasts development are not well characterized. Results: In this study, oscaf2 mutants were obtained by editing the OsCAF2 gene in the Nipponbare variety of rice. Phenotypic analysis showed that mutations to OsCAF2 led to albino leaves at the seeding stage that eventually caused plant death, and oscaf2 mutant plants had fewer chloroplasts and damaged chloroplast structure. We speculated that OsCAF2 might participate in the splicing of group IIA and IIB introns, which differs from its orthologs in A. thaliana and maize. Through yeast two-hybrid experiments, we found that the C-terminal region of OsCAF2 interacted with OsCRS2 and formed an OsCAF2-OsCRS2 complex. In addition, the N-terminal region of OsCAF2 interacted with itself to form homodimers. Conclusion: Taken together, this study improved our understanding of the OsCAF2 protein, and revealed additional information about the molecular mechanism of OsCAF2 in regulating of chloroplast development in rice. Keywords: OsCAF2, CRM domain, Intron splicing, Chloroplast development, Rice Background encoded polymerases (PEPs) and nucleus-encoded poly- Chloroplasts are necessary organelles for plant growth merases (NEPs) play key roles in regulating chloroplast and development, as they biosynthesize carbohydrates development. These studies suggest that expressions of through the fixation of CO2 [1, 2]. Chloroplasts are de- chloroplast genes require proteins encoded by the nu- rived from proplastids and are semiautonomous organ- clear genome [5, 6]. These proteins are involved in the elles [3]. The chloroplast genome is small and encodes transcription and post-transcription modification of approximately 100 proteins responsible largely for chloroplast related genes, such as chloroplast DNA repli- photosynthesis, carbon metabolism, and fatty acid syn- cation, RNA transcription, RNA editing, RNA stability, thesis [4]. Many studies have indicated that plastid- and RNA splicing [6]. The process of RNA splicing occurs by removing in- * Correspondence: [email protected] † trons from the precursor messenger mRNA (pre-mRNA) Lan Shen and Qiang Zhang contributed equally to this work. to join adjacent exons [7]. In plants, the introns of 1State Key Laboratory of Rice Biology / China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China chloroplast genes are divided into two groups, known as Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Shen et al. BMC Plant Biology (2020) 20:381 Page 2 of 11 group I and group II introns, based on their conserved pri- complex, which was required for splicing of five subgroup mary and secondary structures, as well as the splicing IIB introns from the genes ndhA, ndhB, rps12, petB,and mechanism of RNA splicing. Group II introns are further ycf3 [23, 24]. The CFM2 has four CRM domains. In maize, divided into two subgroups, subgroup IIA and subgroup ZmCFM2 was required to splice the trnL, ndhA,andycf3 IIB [7, 8]. Previous work has shown that group I and introns [26]. In A. thaliana, AtCFM2 can splice the trnL, group II introns of chloroplast genes have lost the ability ndhA,andycf3 introns, and it influences splicing of the for autocatalytic splicing, and the introns of these genes clpP intron that was absent from the maize chloroplast lose elements that were necessary for RNA-based catalytic genome [26]. Unlike other proteins contained in the CRM centers [8, 9]. Chloroplast RNA splicing requires the re- domains, CFM3 contains three CRM domains and was lo- cruitment of proteins that are encoded by nuclear genes. cated in both chloroplasts and mitochondria. In A. thali- These proteins act as splicing factors that are essential for ana, AtCFM3a was necessary for splicing of the ndhB chloroplast RNA splicing reactions [7, 10]. In Arabidopsis intron [26]. In rice, fourteen proteins containing one or thaliana, chloroplast genome contains 20 group II introns more CRM domains have been identified [7]. The oscfm3 and 1 group I intron. In maize and rice, the chloroplast mutant resulted in an albino phenotype in seedlings genome consists of 17 group II introns and one group I caused by abnormal chloroplast development. OsCFM3 intron [11]. It has been reported that many nuclear genes promotes splicing of chloroplast genes ndhB, petD,and encode proteins that act as splicing factors that are in- rps16 [26]. Previous research showed that AL2 encodes volved in the regulation of chloroplast RNA splicing. For OsCRS1, which is homologous to AtCRS1 and ZmCRS1, example, pentatricopeptide repeat (PPR) proteins and and contains three CRM domains. However, OsCRS1 pro- chloroplast RNA splicing and ribosome maturation motes splicing of group I (trnL)andgroupIIintrons (CRM) domain proteins are involved in the regulation of (atpF, rpl2, ndhA, ndhB, petD,andycf3)thatdifferfrom splicing of chloroplast gene introns [7]. the homologous proteins AtCRS1 and ZmCRS1 [11]. It Previous studies also showed that many PPR proteins has been reported that OsCAF1 contains two CRM do- participate in the splicing of group II introns in various mains that could interact with OsCRS2 via its C-terminal plant species [12, 13]. For example, in maize, ZmPPR4 region and forms the OsCAF1-OsCRS2 complex in rice. and ZmPPR5 promote intron splicing of rps12 and trnG The OsCAF1 localizes to the chloroplast and affects spli- in the chloroplast [14, 15]. In A. thaliana, AtOTP70 and cing of subgroup IIA and subgroup IIB introns [27]. The AtOTP51 are required for intron splicing of rpoC1 and function of other proteins containing the CRM domain ycf3–2 [16, 17]. In rice, WSL4 and PGL12 participate in has not been studied extensively in rice. intron splicing of rpl2 and ndhA, respectively [18, 19]. In this study, we generated an oscaf2 mutant by using Inactivation of the PPR proteins involved in chloroplast the CRISPR/Cas9 (Clustered Regularly Interspaced Short intron splicing leads to abnormal chloroplast develop- Palindromic Repeats) gene-editing system and studied ment, with leaves showing chlorosis or albino seedling the role of OsCAF2 in rice chloroplast development. phenotypes [20, 21]. Our results showed that mutants of OsCAF2 lead to ab- With the exception of PPR proteins, some CRM normal chloroplast development and albino phenotypes domain-containing proteins act as splicing factors that in seedlings. Analysis of intron splicing of chloroplast regulate the splicing of chloroplast introns. It has been re- genes showed that OsCAF2 promoted the splicing of ported that the CRM domain-containing proteins influ- chloroplast subgroup IIA and subgroup IIB introns, ence chloroplast development in A. thaliana, maize, and which were necessary for chloroplast development. Simi- rice [7]. The first CRM gene, CRS1, was identified and lar to the ZmCAF2-ZmCRS2 complex, the C-terminal cloned in maize. ZmCRS1 contains three CRM domains, region of OsCAF2 interacted with OsCRS2 and formed which have high affinity and specificity in vitro for the the OsCAF2-OsCRS2 complex. Interestingly, OsCAF2 atpF intron, and they participate in intron splicing of atpF also could interact with itself through its N-terminal re- [9, 22]. ZmCAF1 and ZmCAF2 contain two CRM do- gion to form dimers that regulate chloroplast develop- mains, and each of them can interact with ZmCRS2 and ment in rice. These results demonstrate the molecular form ZmCAF1-ZmCRS2 and ZmCAF2-ZmCRS2 com- mechanism of OsCAF2 in rice chloroplast development. plexes [23]. The ZmCAF1-ZmCRS2 complex is required for the splicing of subgroup IIB introns, including rpl16, Results rps16, trnG, petD,andycf3 [24]. In A. thaliana, the Disruption of OsCAF2 function caused an albino AtCAF1-AtCRS2 complex also promoted the splicing of phenotype the rpoC1 and ClpP introns, which were absent in the According to previous studies, the gene homologous to maize chloroplast genome [25]. Furthermore, earlier stud- ZmCAF2 and AtCAF2 from maize and A. thaliana was iden- ies showed that the C-terminal region of ZmCAF2 can tifiedfromthericegenomeandnamedOsCAF2 (LOC_ interact with ZmCRS2 to form the ZmCAF2-ZmCRS2 Os01g21990)[7]. The OsCAF2 contains six exons, with a Shen et al. BMC Plant Biology (2020) 20:381 Page 3 of 11 total coding region of 1824 bp, which encodes 608 amino Expression analysis of chloroplast development and acids.
Load more

Recommended publications
  • Characterization of the CRM Gene Family and Elucidating the Function of Oscfm2 in Rice
    biomolecules Article Characterization of the CRM Gene Family and Elucidating the Function of OsCFM2 in Rice Qiang Zhang y , Lan Shen y, Deyong Ren, Jiang Hu, Li Zhu, Zhenyu Gao, Guangheng Zhang , Longbiao Guo, Dali Zeng and Qian Qian * State Key Laboratory of Rice Biology/China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China; [email protected] (Q.Z.); [email protected] (L.S.); [email protected] (D.R.); [email protected] (J.H.); [email protected] (L.Z.); [email protected] (Z.G.); [email protected] (G.Z.); [email protected] (L.G.); [email protected] (D.Z.) * Correspondence: [email protected]; Tel.: +86-571-6337-0483 These authors contributed equally to this work. y Received: 10 January 2020; Accepted: 17 February 2020; Published: 18 February 2020 Abstract: The chloroplast RNA splicing and ribosome maturation (CRM) domain-containing proteins regulate the expression of chloroplast or mitochondrial genes that influence plant growth and development. Although 14 CRM domain proteins have previously been identified in rice, there are few studies of these gene expression patterns in various tissues and under abiotic stress. In our study, we found that 14 CRM domain-containing proteins have a conservative motif1. Under salt stress, the expression levels of 14 CRM genes were downregulated. However, under drought and cold stress, the expression level of some CRM genes was increased. The analysis of gene expression patterns showed that 14 CRM genes were expressed in all tissues but especially highly expressed in leaves. In addition, we analyzed the functions of OsCFM2 and found that this protein influences chloroplast development by regulating the splicing of a group I and five group II introns.
    [Show full text]
  • ( 12 ) Patent Application Publication ( 10 ) Pub . No .: US 2020/0407740 A1 CUI Et Al
    US 20200407740A1 IN ( 19 ) United States ( 12 ) Patent Application Publication ( 10 ) Pub . No .: US 2020/0407740 A1 CUI et al. ( 43 ) Pub . Date : Dec. 31 , 2020 ( 54 ) MATERIALS AND METHODS FOR Publication Classification CONTROLLING BUNDLE SHEATH CELL ( 51 ) Int. CI . FATE AND FUNCTION IN PLANTS C12N 15/82 ( 2006.01 ) ( 71 ) Applicant: FLORIDA STATE UNIVERSITY ( 52 ) U.S. CI . RESEARCH FOUNDATION , INC . , CPC C12N 15/8225 ( 2013.01 ) ; C12N 15/8269 Tallahassee, FL ( US ) ( 2013.01 ) ; C12N 15/8261 ( 2013.01 ) ( 57 ) ABSTRACT ( 72 ) Inventors : HONGCHANG CUI , The subject invention concerns materials and methods for TALLAHASSEE , FL (US ); DANYU increasing and / or improving photosynthetic efficiency in KONG , BLACKSBURG , VA (US ); plants, and in particular, C3 plants. In particular, the subject YUELING HAO , TALLAHASSEE , FL invention provides for means to increase the number of ( US ) bundle sheath ( BS ) cells in plants , to improve the efficiency of photosynthesis in BS cells , and to increase channels between BS and mesophyll ( M ) cells . In one embodiment, a ( 21 ) Appl . No .: 17 / 007,043 method of the invention concerns altering the expression level or pattern of one or more of SHR , SCR , and / or SCL23 in a plant. The subject invention also pertains to genetically ( 22 ) Filed : Aug. 31 , 2020 modified plants , and in particular, C3 plants, that exhibit increased expression of one or more of SHR , SCR , and / or SCL23 . Transformed and transgenic plants are contemplated Related U.S. Application Data within the scope of the invention . The subject invention also ( 62 ) Division of application No. 14 / 898,046 , filed on Dec. concerns methods for increasing expression of photosyn 11 , 2015 , filed as application No.
    [Show full text]
  • The CRM Domain: an RNA Binding Module Derived from an Ancient Ribosome-Associated Protein
    JOBNAME: RNA 13#1 2007 PAGE: 1 OUTPUT: Thursday December 7 00:09:11 2006 csh/RNA/127813/rna1396 Downloaded from rnajournal.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press The CRM domain: An RNA binding module derived from an ancient ribosome-associated protein ALICE BARKAN,1 LARIK KLIPCAN,2 OREN OSTERSETZER,2 TETSUYA KAWAMURA,1,3 YUKARI ASAKURA,1 and KENNETH P. WATKINS1 1Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1229, USA 2Agricultural Research Organization, Volcani Center, Bet Dagan 50250, Israel ABSTRACT The CRS1–YhbY domain (also called the CRM domain) is represented as a stand-alone protein in Archaea and Bacteria, and in a family of single- and multidomain proteins in plants. The function of this domain is unknown, but structural data and the presence of the domain in several proteins known to interact with RNA have led to the proposal that it binds RNA. Here we describe a phylogenetic analysis of the domain, its incorporation into diverse proteins in plants, and biochemical properties of a prokaryotic and eukaryotic representative of the domain family. We show that a bacterial member of the family, Escherichia coli YhbY, is associated with pre-50S ribosomal subunits, suggesting that YhbY functions in ribosome assembly. GFP fused to a single-domain CRM protein from maize localizes to the nucleolus, suggesting that an analogous activity may have been retained in plants. We show further that an isolated maize CRM domain has RNA binding activity in vitro, and that a small motif shared with KH RNA binding domains, a conserved ‘‘GxxG’’ loop, contributes to its RNA binding activity.
    [Show full text]
  • The Mitochondrial Pentatricopeptide Repeat Protein PPR18 Is Required for the Cis-Splicing of Nad4 Intron 1 and Essential to Seed Development in Maize
    International Journal of Molecular Sciences Article The Mitochondrial Pentatricopeptide Repeat Protein PPR18 Is Required for the cis-Splicing of nad4 Intron 1 and Essential to Seed Development in Maize Rui Liu 1, Shi-Kai Cao 1 , Aqib Sayyed 1, Chunhui Xu 1, Feng Sun 1, Xiaomin Wang 2 and Bao-Cai Tan 1,* 1 Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; [email protected] (R.L.); [email protected] (S.-K.C.); [email protected] (A.S.); [email protected] (C.X.); [email protected] (F.S.) 2 Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; [email protected] * Correspondence: [email protected] Received: 10 May 2020; Accepted: 2 June 2020; Published: 5 June 2020 Abstract: Pentatricopeptide repeat (PPR) protein comprises a large family, participating in various aspects of organellar RNA metabolism in land plants. There are approximately 600 PPR proteins in maize, but the functions of many PPR proteins remain unknown. In this study, we defined the function of PPR18 in the cis-splicing of nad4 intron 1 in mitochondria and seed development in maize. Loss function of PPR18 seriously impairs embryo and endosperm development, resulting in the empty pericarp (emp) phenotype in maize. PPR18 encodes a mitochondrion-targeted P-type PPR protein with 18 PPR motifs. Transcripts analysis indicated that the splicing of nad4 intron 1 is impaired in the ppr18 mutant, resulting in the absence of nad4 transcript, leading to severely reduced assembly and activity of mitochondrial complex I and dramatically reduced respiration rate.
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2016/0115499 A1 CUI Et Al
    US 2016O115499A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2016/0115499 A1 CUI et al. (43) Pub. Date: Apr. 28, 2016 (54) MATERALS AND METHODS FOR Publication Classification CONTROLLING BUNDLE SHEATH CELL FATE AND FUNCTION IN PLANTS (51) Int. Cl. CI2N 5/82 (2006.01) (71) Applicant: FLORIDA STATE UNIVERSITY (52) U.S. Cl. RESEARCH FOUNDATION, INC., CPC ........ CI2N 15/8269 (2013.01); C12N 15/8225 Tallahassee, FL (US) (2013.01) (57) ABSTRACT (72) Inventors: HONGCHANG CUI, TALLAHASSEE, The Subject invention concerns materials and methods for FL (US); DANYUKONG, increasing and/or improving photosynthetic efficiency in BLACKSBURG, VA (US); YUELING plants, and in particular, C3 plants. In particular, the Subject HAO, TALLAHASSEE, FL (US) invention provides for means to increase the number of bundle sheath (BS) cells in plants, to improve the efficiency of (21) Appl. No.: 14/898,046 photosynthesis in BS cells, and to increase channels between BS and mesophyll (M) cells. In one embodiment, a method of (22) PCT Fled: Jun. 11, 2014 the invention concerns altering the expression level or pattern of one or more of SHR, SCR, and/or SCL23 in a plant. The (86) PCT NO.: PCT/US2014/041975 Subject invention also pertains to genetically modified plants, S371 (c)(1), and in particular, C3 plants, that exhibit increased expression (2) Date: Dec. 11, 2015 of one or more of SHR, SCR, and/or SCL23. Transformed and transgenic plants are contemplated within the scope of the invention. The Subject invention also concerns methods for increasing expression of photosynthetically important Related U.S.
    [Show full text]
  • Suppl Figure 1
    Suppl Table 2. Gene Annotation (October 2011) for the selected genes used in the study. Locus Identifier Gene Model Description AT5G51780 basic helix-loop-helix (bHLH) DNA-binding superfamily protein; FUNCTIONS IN: DNA binding, sequence-specific DNA binding transcription factor activity; INVOLVED IN: regulation of transcription; LOCATED IN: nucleus; CONTAINS InterPro DOMAIN/s: Helix-loop-helix DNA-binding domain (InterPro:IPR001092), Helix-loop-helix DNA-binding (InterPro:IPR011598); BEST Arabidopsis thaliana protein match is: basic helix-loop-helix (bHLH) D AT3G53400 BEST Arabidopsis thaliana protein match is: conserved peptide upstream open reading frame 47 (TAIR:AT5G03190.1); Has 285 Blast hits to 285 proteins in 23 species: Archae - 0; Bacteria - 0; Metazoa - 1; Fungi - 0; Plants - 279; Viruses - 0; Other Eukaryotes - 5 (source: NCBI BLink). AT1G44760 Adenine nucleotide alpha hydrolases-like superfamily protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: response to stress; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: UspA (InterPro:IPR006016), Rossmann-like alpha/beta/alpha sandwich fold (InterPro:IPR014729); BEST Arabidopsis thaliana protein match is: Adenine nucleotide alpha hydrolases-li AT4G19950 unknown protein; BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT5G44860.1); Has 338 Blast hits to 330 proteins in 72 species: Archae - 2; Bacteria - 94; Metazoa - 7; Fungi - 0; Plants - 232; Viruses - 0; Other Eukaryotes - 3 (source: NCBI BLink). AT3G14280
    [Show full text]
  • A Plant-Specific RNA-Binding Domain Revealed Through Analysis of Chloroplast Group II Intron Splicing
    A plant-specific RNA-binding domain revealed through analysis of chloroplast group II intron splicing Tiffany S. Kroegera,1, Kenneth P. Watkinsa,1, Giulia Frisob, Klaas J. van Wijkb, and Alice Barkana,2 aInstitute of Molecular Biology, University of Oregon, Eugene, OR 97403; and bDepartment of Plant Biology, Cornell University, Ithaca, NY 14853 Edited by Alan M. Lambowitz, University of Texas, Austin, TX, and approved January 7, 2009 (received for review December 8, 2008) Comparative genomics has provided evidence for numerous con- members of the DUF860 family are predicted to localize to served protein domains whose functions remain unknown. We chloroplasts or mitochondria, suggesting that proteins with this identified a protein harboring ‘‘domain of unknown function 860’’ domain have multiple roles in gene expression in both organelles. (DUF860) as a component of group II intron ribonucleoprotein Although DUF860 is found only in land plants, it is distantly particles in maize chloroplasts. This protein, assigned the name related to a class of ubiquitin hydrolases (UBH) found through- WTF1 (‘‘what’s this factor?’’), coimmunoprecipitates from chloro- out the eucaryotes. However, structural modeling suggests that plast extract with group II intron RNAs, is required for the splicing DUF860 adopts a structure that differs from UBH enzymes, and of the introns with which it associates, and promotes splicing in the that has a surface that is reminiscent of helical repeat RNA- context of a heterodimer with the RNase III-domain protein RNC1. binding motifs such as the PPR and PUM-HD motifs. Both WTF1 and its resident DUF860 bind RNA in vitro, demonstrat- ing that DUF860 is a previously unrecognized RNA-binding domain.
    [Show full text]
  • A Nuclear-Encoded Chloroplast Protein Harboring a Single CRM Domain
    Lee et al. BMC Plant Biology 2014, 14:98 http://www.biomedcentral.com/1471-2229/14/98 RESEARCH ARTICLE Open Access A nuclear-encoded chloroplast protein harboring a single CRM domain plays an important role in the Arabidopsis growth and stress response Kwanuk Lee1, Hwa Jung Lee1, Dong Hyun Kim1, Young Jeon2, Hyun-Sook Pai2 and Hunseung Kang1* Abstract Background: Although several chloroplast RNA splicing and ribosome maturation (CRM) domain-containing proteins have been characterized for intron splicing and rRNA processing during chloroplast gene expression, the functional role of a majority of CRM domain proteins in plant growth and development as well as chloroplast RNA metabolism remains largely unknown. Here, we characterized the developmental and stress response roles of a nuclear-encoded chloroplast protein harboring a single CRM domain (At4g39040), designated CFM4, in Arabidopsis thaliana. Results: Analysis of CFM4-GFP fusion proteins revealed that CFM4 is localized to chloroplasts. The loss-of-function T-DNA insertion mutants for CFM4 (cfm4) displayed retarded growth and delayed senescence, suggesting that CFM4 plays a role in growth and development of plants under normal growth conditions. In addition, cfm4 mutants showed retarded seed germination and seedling growth under stress conditions. No alteration in the splicing patterns of intron-containing chloroplast genes was observed in the mutant plants, but the processing of 16S and 4.5S rRNAs was abnormal in the mutant plants. Importantly, CFM4 was determined to possess RNA chaperone activity. Conclusions: These results suggest that the chloroplast-targeted CFM4, one of two Arabidopsis genes encoding a single CRM domain-containing protein, harbors RNA chaperone activity and plays a role in the Arabidopsis growth and stress response by affecting rRNA processing in chloroplasts.
    [Show full text]
  • Supplemental Tables
    SUPPLEMENTAL TABLES Table S1 Table S1. Genes differentially regulated in yda11 1 day after PcBMM inoculation. AGI ID Fold change1 Gene description AT3G10930 16,607 unknown protein AT1G73260 7,619 ATKTI1, KTI1, kunitz trypsin inhibitor 1 AT5G47230 6,857 ATERF-5, ATERF5, ERF5, ethylene responsive element binding factor 5 AT3G04640 6,748 glycine-rich protein AT1G76650 6,690 CML38, calmodulin-like 38 AT3G19580 6,101 AZF2, ZF2, zinc-finger protein 2 AT3G55980 5,941 ATSZF1, SZF1, salt-inducible zinc finger 1 AT2G41640 5,550 Glycosyltransferase family 61 protein AT1G35210 5,488 unknown protein AT1G68765 5,240 IDA, INFLORESCENCE DEFICIENT IN ABSCISSION AT2G35730 5,004 Heavy metal transport/detoxification superfamily protein AT2G31945 4,675 unknown protein AT3G14470 4,568 NB-ARC domain-containing disease resistance protein AT2G28400 4,536 Protein of unknown function, DUF584 AT5G07010 4,505 ATST2A, ST2A, sulfotransferase 2A AT5G09800 4,327 ARM repeat superfamily protein AT4G34150 4,318 Calcium-dependent lipid-binding (CaLB domain) family protein AT3G04070 4,280 anac047, NAC047, NAC domain containing protein 47 AT5G49680 4,090 KIP, Golgi-body localisation protein domain ;RNA pol II promoter Fmp27 protein domain AT1G51915 4,038 cryptdin protein-related AT2G39380 3,818 ATEXO70H2, EXO70H2, exocyst subunit exo70 family protein H2 AT4G31950 3,810 CYP82C3, cytochrome P450, family 82, subfamily C, polypeptide 3 AT4G24110 3,748 unknown protein AT4G00700 3,684 C2 calcium/lipid-binding plant phosphoribosyltransferase family protein AT2G37980 3,680 O-fucosyltransferase
    [Show full text]
  • NIH Public Access Author Manuscript Acta Histochem
    NIH Public Access Author Manuscript Acta Histochem. Author manuscript; available in PMC 2015 October 01. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Acta Histochem. 2014 October ; 116(8): 1307–1312. doi:10.1016/j.acthis.2014.08.001. Identification of two novel type 1 peroxisomal targeting signals in Arabidopsis thaliana Rigoberto A. Ramirez, Brian Espinoza, and Ernest Y. Kwok* Department of Biology, California State University Northridge, 18111 Nordhoff St. Northridge, CA 91330, USA Abstract Peroxisomes lack their own genetic material and must therefore import proteins encoded by genes in the nucleus. Amino acids within these proteins serve as targeting signals: they direct the delivery of the proteins to the organelle. The majority of soluble proteins destined for the peroxisomal matrix utilize a type 1 peroxisomal targeting signal (PTS1): a C-terminal tripeptide that follows the pattern small/basic/hydrophobic. We have discovered two new C-terminal tripeptides that target proteins to peroxisomes in Arabidopsis thaliana. The tripeptides PSL and KRR do not fit the major PTS1 consensus but cause green fluorescent protein to accumulate in peroxisomes of stably transformed Arabidopsis. We have identified forty-one proteins in the Arabidopsis genome that also bear these tripeptides at their C-termini and may therefore be peroxisomal. Keywords Peroxisome; PTS1; Arabidopsis thaliana Introduction Peroxisomes are single membrane bounded organelles found in nearly all eukaryotes (Schluter et al., 2006). In plants, the dominant functions of peroxisomes are photorespiration and β-oxidation of fatty acids. Peroxisomes also play important roles in a number of other metabolic pathways including synthesis of the hormones jasmonic acid and auxin (reviewed in Hu et al., 2012).
    [Show full text]
  • Sensing and Retrograde Signalling of Mitochondrial Metabolic States in Plants
    Sensing and Retrograde Signalling of Mitochondrial Metabolic States in Plants Dissertation der Fakultät für Biologie der Ludwig-Maximilians-Universität München Vorgelegt von Ann-Christine König München, Juni 2014 Gutachter: Dr. Iris Finkemeier (Erstgutachter) Prof. Dr. Jörg Nickelsen (Zweitgutachter) Prof. Dr. Wolfgang Enard Prof. Dr. Thorsten Mascher PD. Dr. Bolle Prof. Dr. Günther Heubl Tag der Dissertations Abgabe: 18.06.2014 Tag der mündlichen Prüfung: 26.09.2014 Table of contents I. Summary 3 II. Zusammenfassung 5 III. Aim of Thesis 7 IV. List of Publications 9 V. Abbreviations 11 1. General Introduction 13 1.1 Main function of mitochondria in plants cells 14 1.2. Mitochondrial retrograde signaling in plants 16 1.3. Protein posttranslational modifications connected to mitochondrial metabolism 18 2. Summarizing Discussion 23 2.1. Dysfunctions in mitochondria result in transcriptional changes of distinct metabolic and regulatory pathways 23 2.2. Carboxylic acid treatment results in distinct changes of nuclear transcripts 26 2.3. Correlation between MRR and citrate-dependent transcriptional changes 31 2.4. Redox regulation of mitochondrial citrate synthase 33 2.5. Acetyl-CoA dependent lysine acetylation of mitochondrial proteins 35 2.6. The Arabidopsis sirtuin SRT2 fine tunes mitochondrial metabolism 40 3. Conclusion and Outlook 43 3.1. Future perspectives of transcriptional regulation triggered by citrate 44 3.2. Research outlook for lysine acetylation on metabolic enzymes 45 4. References 47 VI. Declaration of Own Contributions 57 VII. Curriculum Vitae 59 VIII. Eidesstattliche Erklärung 63 IX. Acknowledgements 65 X. Publications 1-7 67 I. Summary I. Summary Plants are exposed to always changing environmental conditions because of their sessile nature.
    [Show full text]
  • Emerging Roles of RNA-Binding Proteins in Plant Growth, Development, and Stress Responses
    Mol. Cells 2016; 39(3): 179-185 http://dx.doi.org/10.14348/molcells.2016.2359 Molecules and Cells http://molcells.org Established in 1990 Emerging Roles of RNA-Binding Proteins in Plant Growth, Development, and Stress Responses Kwanuk Lee, and Hunseung Kang* Posttranscriptional regulation of RNA metabolism, includ- cluding RNA-recognition motif (RRM), zinc finger motif, K ho- ing RNA processing, intron splicing, editing, RNA export, mology (KH) domain, glycine-rich region, arginine-rich region, and decay, is increasingly regarded as an essential step RD-repeats, and SR-repeats (Alba and Pages, 1998; Lorković for fine-tuning the regulation of gene expression in eukar- and Barta, 2002). Plant genomes encode a variety of RBPs, yotes. RNA-binding proteins (RBPs) are central regulatory which suggests the functional diversity of RBPs in plant growth, factors controlling posttranscriptional RNA metabolism development, and stress responses (Lorković, 2009; Mangeon during plant growth, development, and stress responses. et al., 2010). In particular, those RBPs harboring an RRM at the Although functional roles of diverse RBPs in living organ- N-terminus and a glycine-rich region at the C-terminus, thus isms have been determined during the last decades, our referred to as glycine-rich RBP (GRP), zinc finger-containing understanding of the functional roles of RBPs in plants is GRP (RZ), cold shock domain protein (CSDP), and RNA hel- lagging far behind our understanding of those in other icase (RH) have been implicated to play crucial roles in plant organisms, including animals, bacteria, and viruses. How- growth and stress responses (Jankowsky, 2011; Jung et al., ever, recent functional analysis of multiple RBP family 2013; Mihailovich et al., 2010).
    [Show full text]